tbuckley/cabot-search huggingface dataset:
Abstract 2324: Small-scale microwave-assisted acid hydrolysis method for glycogen determination and turnover in tumors using Stable Isotope Resolved Metabolomics
Authors: Andrew N. Lane, Timothy L. Scott, Juan Zhu, Teresa A. Cassel, Sara Vicente-Munoz, Penghui Lin, Richard M. Higashi, Teresa W-M Fan
Journal: Cancer Research (2022)

Abstract Introduction: Glycogen is a readily deployed intracellular energy storage macromolecule composed of branched chains of glucose. Although glycogen primarily occurs in the liver and muscle, it can be found in most tissues throughout the body, and its metabolism has been shown to be important in cancers and immune cells. Robust analysis of glycogen turnover requires stable isotope tracing plus a reliable means of quantifying total and labeled glycogen derived from precursors such as 13C6-glucose. Current methods for analyzing glycogen are time- and sample-consuming, at best semi-quantitative, and unable to measure stable isotope enrichment. Methods: We have developed a microscale method for quantifying both intact and acid-hydrolyzed glycogen by ultra-high-resolution Fourier transform mass spectrometric (UHR-FTMS) and/or NMR analysis in stable isotope resolved metabolomics (SIRM) studies. Polar metabolites, including intact glycogen and their 13C positional isotopomer distributions were first measured in crude biological extracts by high resolution NMR, followed by rapid and efficient acid hydrolysis to glucose in 1 N HCl for 10 minutes at 110 °C under a N2 atmosphere in a microwave-assisted synthesis reactor. The resulting glucose and its 13C isotopologues were then analyzed by UHR-FTMS and/or NMR. Results: We optimized the microwave digestion time, temperature, and oxygen purging in terms of recovery versus degradation and found 10 minutes at 110-115 °C to give &amp;gt; 90% recovery. The method was applied to track the fate of 13C6-glucose in primary human lung BEAS-2B cells, human macrophages, murine liver and patient-derived tumor xenograft (PDTX) in vivo, and the fate of 2H7-glucose in ex vivo lung organotypic tissue cultures of a lung cancer patient. We showed the incorporation of 13C6-glucose into glycogen and its metabolic intermediates, UDP-Glucose and glucose-1-phosphate, both in terms of the 13C levels and fractional enrichment, thereby demonstrating the utility of the method in tracing glycogen turnover in cells and tissues. Conclusions: The method offers a quantitative, sensitive, and convenient means to analyze glycogen turnover in mg amounts of complex biological materials. Keywords: glycogen turnover; 13C6-glucose, stable isotope resolved metabolomics (SIRM); microwave-assisted hydrolysis. Citation Format: Andrew N. Lane, Timothy L. Scott, Juan Zhu, Teresa A. Cassel, Sara Vicente-Munoz, Penghui Lin, Richard M. Higashi, Teresa W-M Fan. Small-scale microwave-assisted acid hydrolysis method for glycogen determination and turnover in tumors using Stable Isotope Resolved Metabolomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2324.
Abstract 5732: <i>p53</i> deficiency causes <i>Myc</i> dysregulation through a novel TGFβ-facilitated promoter switching mechanism to instigate osteosarcoma development
Authors: Yuki Date, Tomoya Ueno, Kosei Ito
Journal: Cancer Research (2022)

Abstract p53 deficiency and Myc dysregulation, driven by genetic and epigenetic alterations, respectively, are frequently associated with cancer. Previously, we reported that the combination of p53 inactivation and Myc overexpression, mediated by Runx transcription factors (TFs), leads to osteosarcoma (OS), the most common primary bone cancer. However, the mechanisms leading to Myc upregulation by Runx in a p53-deficient microenvironment remain unclear. TGFβ is a main driver of the epithelial-to-mesenchymal transition and its signal-dependent TFs, Smads, are known to associate with lineage-determining TFs including Runx. As TGFβ paracrine signalling is reportedly increased during human OS development, we immunodetected increased co-expression of TGFβ and phospho-Smad2 in the bone marrow of osteoprogenitor-specific p53 knockout mice, Osterix (Osx)/Sp7-Cre; p53fl/fl mice, which are widely used as an animal model of human OS. Heterozygous deletion of the type II TGFβ receptor in those mice weakened their susceptibility to OS, phenocopying the overall life-extending effect of Myc depletion in the same model. p53 disruption caused TGFβ to aberrantly induce Myc in osteoprogenitors, rendering the cells tumorigenic upon transplantation into immunocompromised mice. Within the 3-Mb Myc regulatory region, we identified a TGFβ-responsive element dubbed m340, which contains binding sites for multiple TFs including Runx. The m340 enhancer caused Myc upregulation upon p53 disruption by switching its associated promoter from the lncRNA Pvt1 to Myc. In support of this promoter switching mechanism, a specific disruption of the evolutionarily conserved p53 site within the Pvt1 promoter recapitulated TGFβ-induced Myc overexpression. At m340, TGFβ promoted its occupancy by a transcriptional complex consisting of Runx, its cooperative factors Smads and AP1, and CBP, further activating the enhancer by increasing H3K27ac deposition. Runx inhibition not only repressed the aberrant upregulation of Myc by reducing Smad occupancy at m340, but also suppressed OS development in vivo. These results suggest that p53 deficiency causes Myc dysregulation through a novel promoter switching programme that is facilitated by TGFβ signalling and reveals a novel epigenetic mechanism underlying the interaction between cancer-predisposing genetic alterations (p53 deficiency) and environmental cues (TGFβ) in tumorigenesis. Considering the mediating role Runx plays in m340 activation, our study may provide a clinical rationale for targeting Runx in p53-deficient malignancies. Citation Format: Yuki Date, Tomoya Ueno, Kosei Ito. p53 deficiency causes Myc dysregulation through a novel TGFβ-facilitated promoter switching mechanism to instigate osteosarcoma development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5732.
Abstract 208: Peposertib-induced senescence primes irradiated p53 wild-type cancer cells for clearance by both immune cells and senolytic drugs
Authors: Michael Carr, Qing Sun, Chien-Fei Lee, Frank T. Zenke, Andree Blaukat, Lyubomir T. Vassilev
Journal: Cancer Research (2022)

Abstract Peposertib (previously known as M3814) is a potent and selective DNA-PK inhibitor in early-stage clinical development. It effectively blocks the non-homologous end-joining pathway for repair of DNA double-strand breaks (DSB) and has shown strong synergy with ionizing radiation (IR) and DSB-inducing chemotherapy. We recently reported that M3814 overactivates the ATM/p53 signaling axis, reinforces cell cycle checkpoint arrest, and promotes durable premature senescence in irradiated p53 wild-type cancer cells. This unique property of peposertib permits to turn the bulk of irradiated cancer cells into nearly uniform senescent cell population. Using this experimental model, we examined the immunological effects and potential therapeutic applications of IR+peposertib induced senescence. Gene expression analyses of IR+peposertib treated A549 cells showed activation of multiple immune-related genes in the senescent cells, consistent with a strong STING-driven inflammatory response. Multiple secreted cytokines were found substantially elevated in culture media compared to IR controls. Co-culture of IR+peposertib induced senescent cells with PBMCs from healthy volunteers coupled with FACS analyses and live imaging revealed stimulation of the T-cell compartment and killing of senescent but not control cells. Further co-culture experiments with isolated NK cells showed accelerated killing of the senescent IR+peposertib treated A549 cells as compared to controls. These results indicated that IR+peposertib induced inflammatory signaling in senescent A549 cells can stimulate an immune response in vitro, resulting in the effective elimination of both treated and naive A549 cells. We also explored a pharmacological "two-hit" approach. Viability assays and time-lapse imaging showed that the senescent, IR+peposertib treated A549 cells were sensitive to several reported senolytic agents. Of those, the BCL-XL inhibitor A-1331852 was most effective at killing peposertib-promoted senescent A549 cells. Our experiments revealed that selective inhibition of DNA-PK in irradiated p53 wild-type cancer cells provides a powerful mechanism for induction of senescent cancer cells with an immunostimulatory secretory phenotype in vitro. In addition, these cells can be selectively targeted by senolytic agents, suggesting that triple combination radiotherapy with DNA-PK inhibitors and senolytics could offer a potential new approach to the treatment of locally advanced tumors. Citation Format: Michael Carr, Qing Sun, Chien-Fei Lee, Frank T. Zenke, Andree Blaukat, Lyubomir T. Vassilev. Peposertib-induced senescence primes irradiated p53 wild-type cancer cells for clearance by both immune cells and senolytic drugs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 208.
Abstract 5845: The fusion gene landscape in Chinese patients with non-small cell lung cancer
Authors: qiuju lin, Zhichao Fu
Journal: Cancer Research (2022)

Abstract Background: Gene fusion is one of the common types of pathogenic mutation in non-small cell lung cancer(NSCLC). Numerous fusion genes have been identified as important biomarkers and therapeutic targets in NSCLC. The identification and analysis of fusion genes will provide important insights into the mechanisms of NSCLC development and devise novel therapeutic strategies. Here, our primary objective was to describe the landscape of fusion in Chinese patients with NSCLC to explore the new treatment option in NSCLC. Methods: A total of 1192 pathologically confirmed NSCLC samples were collected. The fusion genes were detected using next-generation sequence(NGS). Results: A total of 168 fusion events (14.1%) were identified in 1,192 patients with NSCLC. The most common type of fusion was ALK (64.9%), RET (25%), ROS (8.93%), NTRK1 (3.57%), and FGFR3 (3.57%). In these cases, 109 patients exhibited ALK fusion, including EML4/ALK (97.2%), KIF5B/ALK (0.92%), KLC1/ALK (0.92%), and STRN/ALK (0.92%). A total of 42 patients had RET fusions, of which 83.3%, 11.9%, 2.38%, and 2.38% with KIF5B, CCDC6, GOPC, and TET1 respectively. Notably, RET gene fusions with GOPC (GOPC/RET1), TET1 (TET1/RET1) were first reported in NSCLC and the two novel fusions retained the complete kinase domain of RET. We also found three types of ROS fusions in 15 patients, CD74/ROS1(66.7%) and EZR/ROS1(20%) were the common fusions. Additionally, a new fusion LRIG3/ROS1 which retained the complete kinase domain was identified for the first time in NSCLC patients. Conclusions: We conducted a comprehensive review of fusion genes in Chinese patients with NSCLC. With the exception of common gene fusions, we found three cases of rare fusion mutations, which help to understand the potential pathogenic mechanisms of NSCLC and translate into therapeutic applications. Citation Format: qiuju lin, Zhichao Fu. The fusion gene landscape in Chinese patients with non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5845.
Abstract 5582: Modulation of intracellular kinase signaling to improve TIL manufacturing for adoptive cell therapy
Authors: Zixiao Shi, Sheng Yao, Peipei Zhao, Fei Li, Di Zhou, Jun Cui, Jingwei Sun, Yarong Liu
Journal: Cancer Research (2022)

Abstract Tumor-infiltrating lymphocytes (TILs) has demonstrated significant clinical benefits for patients with solid tumor. A robust expansion process is needed in order to produce a large number of cells for clinical usage. We modulated the PI3K-AKT signaling pathway in TILs isolated from cervical and ovarian cancer patients and found the inhibition of either PI3K or AKT can promote TIL proliferation during the REP stage. Inhibiting PI3K-AKT led to an increase of the effector CD8+T cell population with higher CD25+ and CD28+ in the CD8+ population, more TCF-1+ and CD39-CD69- T cells in both CD4+ and CD8+ T cell population, and downregulated exhaustion markers CD39+ and TIM-3+ in CD8+ T cell population. This inhibition significantly increased cytotoxicity when cocultured with tumor cell lines and patient-derived tumor samples. Moreover, dual knockout of ATK1 and ATK2 promoted TIL proliferation, long-term survival and decreased apoptosis of TIL, which were further confirmed by the RNA-seq results. Thus, inhibition of PI3K-AKT signaling represents a promising strategy to generate large numbers of TIL with enhanced stemness, activation and cytotoxicity, and could be used to support adoptive cell therapy to treat solid tumors. Citation Format: Zixiao Shi, Sheng Yao, Peipei Zhao, Fei Li, Di Zhou, Jun Cui, Jingwei Sun, Yarong Liu. Modulation of intracellular kinase signaling to improve TIL manufacturing for adoptive cell therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5582.
Abstract PL01-05: Genomic medicine meets cancer interception
Authors: Susan M. Domchek
Journal: Cancer Research (2022)

Abstract The increased identification of individuals with an elevated risk of developing cancer based on inherited genetic susceptibility allows for targeted cancer interception opportunities. Understanding the molecular basis for cancer susceptibility creates the potential to disrupt the oncogenic process even after it has started. Individuals with pathogenic variants in BRCA1 and BRCA2 are at increased risk for the development of breast, ovarian, pancreatic, and prostate cancers. Work over the past decade has allowed for an understanding of the cells of origin of BRCA1 - related breast cancer and has led to a Phase III study of denosumab vs placebo to examine the impact of denosumab on breast cancer risk. The adjuvant study of the PARP inhibitor olaparib in high risk BRCA-associated breast cancer demonstrated an improvement in event free survival along with a favorable safety profile, paving the way for further work in the prevention space. Immunologic approaches have led to clinical trials using vaccines which will include healthy BRCA1/2 carriers. As our molecular understanding of BRCA haploinsufficiency improves, so too will our options for cancer interception. All of this work could lead to a halo effect with impact on sporadic cancer interception. Citation Format: Susan M. Domchek. Genomic medicine meets cancer interception [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr PL01-05.
Abstract 1525: Inhibition of HGF maturation overcomes cetuximab resistance in colorectal cancer
Authors: Ramona Graves-Deal, Galina Bogatcheva, Vivian T. Truong, Vishnu Damalanka, Lidija Klampfer, Robert J. Coffey, James W. Janetka, Bhuminder Singh
Journal: Cancer Research (2022)

Abstract We have previously identified that activation of receptor tyrosine kinases (RTKs) MET and RON contributed to resistance to the EGF receptor (EGFR)-directed therapeutic antibody cetuximab. These findings originated from our in vitro 3D type I collagen cultures of human colorectal cancer (CRC) cell line HCA-7 derivatives CC, SC, and CC-CR. CC are sensitive to cetuximab, while SC and CC-CR are resistant. Both de novo and acquired modes of cetuximab resistance in SC and CC-CR, respectively, could be overcome by crizotinib, a multi-RTK inhibitor that also targets MET and RON. Conversely, exogenous administration of MET ligand, HGF could transiently induce cetuximab resistance which could be further overcome by crizotinib addition. HGF/HGFL are synthesized as inactive precursors and require cleavage by proteases (HGFA, Matriptase, and Hepsin) to be biologically active. To inhibit HGF/HGFL cleavage in cetuximab-resistant cells, we employed inhibitors of HGF/HGFL proteases (ZFH7116 and VD2173) and were able to overcome both de novo and acquired cetuximab resistance. A survey of TCGA datasets indicated that HGF/HGFL were overexpressed in several CRC CMS subtypes. We next expressed human HGF in cetuximab-sensitive CC cells and observed that HGF overexpression imparts cetuximab resistance. Moreover, cetuximab resistance induced by HGF overexpression could be overcome by the downstream MET inhibition (with crizotinib) and we are now testing if the upstream inhibition of HGF proteases (with ZFH7116/VD2173) also overcomes cetuximab resistance. Combined these results indicate that inhibition of HGF cleavage and maturation may be a novel way to overcome resistance to EGFR-targeted therapies in CRC. Citation Format: Ramona Graves-Deal, Galina Bogatcheva, Vivian T. Truong, Vishnu Damalanka, Lidija Klampfer, Robert J. Coffey, James W. Janetka, Bhuminder Singh. Inhibition of HGF maturation overcomes cetuximab resistance in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1525.
Abstract 2242: Impact of low-dose computed tomography screening for lung cancer at a community oncology clinic on stage of lung cancer diagnosis in the catchment area
Authors: Edgar T. Ellis, Michael A. Bauer, Thaddeus Beck, Daniel S. Bradford, Joanna Thompson, Margarete C. Kulik, Joseph L. Su
Journal: Cancer Research (2022)

Abstract Introduction: Arkansas has the second-highest incidence of lung cancer in the U.S., with a largely rural and medically underserved population. Low-dose computed tomography (LDCT) is a well-established procedure for lung cancer screening in academic medical centers, but few local community oncology centers utilize this technology. Highlands Oncology Group (HOG), located in Northwest Arkansas (NWA), took the initiative to bring LDCT screening to a non-academic medical center and provide routine LDCT screening to a rural population. The objective of this study is to evaluate the benefits of free LDCT screening at a community oncology clinic. Methods: The study compared for-fee and free periods of LDCT screening at HOG and their impact on identifying cancer in NWA. The study population was patients in HOG’s catchment area who fell into the risk categories set by the National Comprehensive Cancer Network Clinical Practice Guidelines in Oncology to be eligible for screening between March 2013 and February 2020. Results: A total of 5,402 eligible participants enrolled in the study. During ten months of for-fee screening (n=60), 3.3% of patients diagnosed had Stage I lung cancer, and 1.7% were diagnosed with Stages II-IV. During the first ten months of free screening (n=729), 3% of patients were diagnosed with Stage I lung cancer, 1.8% were diagnosed with Stages II-IV, and 1.1% were diagnosed with other cancers. Over the entire program until February 2020 (n=5,402), a total of 76 patients were diagnosed with Stage I lung cancer, 52 were diagnosed with Stage II-IV, and 35 were diagnosed with other cancers. Conclusion: The result of this study suggests that eligible patients are more receptive to free lung cancer screening, even though most insurance coverage does not have a required co-pay for eligible patients. We also observed an increased diagnosis rate for early-stage lung cancers due to increased patient influx with free LDCT screening. The state central registry data showed a decline in distant lung cancer after the free LDCT screening offered in the northwestern counties in the HOG catchment area. At the same time, no such trend is visible for the entire state, suggesting a stage shift in lung cancer due to free LDCT screening. Citation Format: Edgar T. Ellis, Michael A. Bauer, Thaddeus Beck, Daniel S. Bradford, Joanna Thompson, Margarete C. Kulik, Joseph L. Su. Impact of low-dose computed tomography screening for lung cancer at a community oncology clinic on stage of lung cancer diagnosis in the catchment area [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2242.
Abstract 237: Evaluation of cell membrane lipid-extracted nanoliposomes (CLENs) as a potential drug platform for targeting multiple myeloma
Authors: Christina T. Tran, Eden Park, Pedro L. Rodriguez-Flores, Robert B. Campbell
Journal: Cancer Research (2022)

Abstract Background: Multiple myeloma (MM) is a plasma cell malignancy that primarily affects the elderly. MM is the second most common hematologic cancer with approximately 25,000-30,000 new cases diagnosed annually in the United States. A challenge associated with MM therapy is unwanted drug uptake by normal healthy cells. Nanoparticles provide a promising outlook to mitigate these issues, offering more selective drug uptake, while minimizing toxicity associated with treatment. The objective of this study was to develop, optimize and evaluate physicochemical and In vitro properties of MM-CLENs in comparison to conventional liposomes and relevant cell controls. Methods: RPMI-8226 MM cell line was selected cellular model for MM disease. RPMI-8226 cells were cultured and expanded In vitro for cellular extraction purposes. Lipid extraction (LE) procedures were performed to generate the RPMI-8226 LE ingredient. Other lipid ingredients used in preparation of RPMI-8226 CLENs included DOPC, cholesterol, and DPPE-Rhodamine (fluorescence indicator). Phase I included physicochemical characterization and cellular uptake studies of CLENs preparations with varying concentration of RPMI-8226-LE (0 to 40 mol%) content. Phase II began with the optimized concentration of LE determined in Phase I, along with varying concentrations of cholesterol (0 to 40 mol %) content for the nano-targeting studies in vitro. The control cell lines represent other hematological diseases, K-562-GFP (chronic myeloid leukemia), CCRF-CEM (acute lymphoblastic leukemia), and U937 (lymphoma). Results: Phase I and II physicochemical characterization and In vitro studies, revealed that the optimized preparation of RPMI-8226-CLENs consisted of 5% LE, and 5% cholesterol content. Optimal preparation consisted of DOPC: Cholesterol: LE (90:5:5) with an average values for particle size and zeta potential of 178±38 nm (n=4), and -14±4 mV (n=4), respectively. The inclusion of LE in conventional DOPC:cholesterol liposomes resulted in significantly improved uptake of the CLENs by RPMI-8226 cells in vitro (P&amp;lt; 0.001). However, preliminary selectivity studies suggest no significant difference in the uptake of RPMI-8226-CLENs by RPMI-8226 when compared to control cells (K-562-GFP, CCRF-CEM and U937). Conclusion: Studies involving RPMI-8226 CLENs are currently underway. Such studies include target selectivity, and influence of additional components of CLENs as a function of the microenvironment. Citation Format: Christina T. Tran, Eden Park, Pedro L. Rodriguez-Flores, Robert B. Campbell. Evaluation of cell membrane lipid-extracted nanoliposomes (CLENs) as a potential drug platform for targeting multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 237.